X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=cd305436a35c7d9cf68addb95e2be421caa53bee;hb=1d123ffc99d3e9fb14dd1440adcd8d60a938722f;hp=8398643c3bede3aca4e031f245c3f790e3d56103;hpb=9e896372d111e5b6090ce211e06c6c6e5c4a75fa;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 8398643..cd30543 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -22,13 +22,21 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
   ColourSchemeI oldColourScheme;
   JInternalFrame frame;
 
-
-  public UserDefinedColours(JInternalFrame f, AlignmentPanel ap, SequenceGroup sg)
+  public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
   {
     super();
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    Desktop.addInternalFrame(frame, "User defined colours", 450,530, false );
+    if(System.getProperty("os.name").startsWith("Mac"))
+      frame.setSize(450,560);
+
+    if(sg!=null)
+        frame.setTitle( frame.getTitle()+ " ("+sg.getName()+")");
+
     colorChooser.getSelectionModel().addChangeListener(this);
+
     this.ap = ap;
-    frame = f;
     seqGroup = sg;
 
 
@@ -44,14 +52,12 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
       makeButton("B", "B");
       makeButton("Z", "Z");
       makeButton("X", "X");
-      makeButton("'.','-',' '", "-");
+      makeButton("Gap", "'.','-',' '");
 
       if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
       {
         loadColour(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
       }
-
-
   }
 
  public void stateChanged(ChangeEvent evt)
@@ -73,7 +79,7 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
 
 
     try{
-      col = oldColourScheme.findColour(aa, -1, null);
+      col = oldColourScheme.findColour(aa, -1);
     }catch(Exception ex){}
 
     button.setBackground(  col );
@@ -89,7 +95,7 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
       }
     });
 
-    buttonPanel.add(button);
+    buttonPanel.add(button, null);
   }
 
 
@@ -103,7 +109,7 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
 
   protected void applyButton_actionPerformed(ActionEvent e)
   {
-    UserColourScheme ucs = new UserColourScheme();
+
     Color [] newColours = new Color[24];
     for(int i=0; i<24; i++)
     {
@@ -111,6 +117,7 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
           newColours[i] = button.getBackground();
     }
 
+    UserColourScheme ucs = new UserColourScheme();
     ucs.setThreshold(0);
     ucs.setColourScheme( newColours );
 
@@ -119,7 +126,7 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
     else
       ap.av.setGlobalColourScheme(ucs);
 
-    ap.RefreshPanels();
+    ap.repaint();
   }
 
   protected void loadbutton_actionPerformed(ActionEvent e)
@@ -139,6 +146,29 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
 
   }
 
+  public static UserColourScheme loadDefaultColours(String file)
+  {
+    UserColourScheme ucs = null;
+    try
+    {
+      BufferedReader in = new BufferedReader(new FileReader(file));
+      Color [] newColours = new Color[24];
+      for (int i = 0; i < 24; i++)
+      {
+        newColours[i] = new Color(Integer.parseInt(in.readLine()));
+      }
+
+      ucs = new UserColourScheme();
+      ucs.setThreshold(0);
+      ucs.setColourScheme(newColours);
+
+    }
+    catch (Exception ex)
+    {}
+
+    return ucs;
+  }
+
   void loadColour(String file)
   {
     try
@@ -150,6 +180,8 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
         Color c = new Color(Integer.parseInt(in.readLine()));
         button.setBackground(c);
       }
+
+      jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", file);
     }
     catch (Exception ex)
     {}
@@ -200,8 +232,11 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
     else
       ap.av.setGlobalColourScheme(ucs);
 
-    ap.RefreshPanels();
+    ap.repaint();
 
+    try{
+      frame.setClosed(true);
+    }catch(Exception ex){}
   }